Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 111 of 120
Found at i:32892790 original size:28 final size:28
Alignment explanation
Indices: 32892741--32892796 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
32892731 TTAAATTAAA
*
32892741 ATTTTATTATTTTAAGAATTAAAGTATT
1 ATTTTATTATTTTAAGAATTAAAATATT
**
32892769 ATTTTA-TATTTTACTAATTTAAAATATT
1 ATTTTATTATTTTAAGAA-TTAAAATATT
32892797 GTAAAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
ATTTTATTATTTTAAGAATTAAAATATT
Found at i:32894708 original size:4 final size:4
Alignment explanation
Indices: 32894701--32894725 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
32894691 CATACATACT
32894701 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
32894726 CATGTGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:32900754 original size:31 final size:28
Alignment explanation
Indices: 32900719--32900813 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 28
32900709 ATCAAAACCG
32900719 AAGTTTCATGTATACATTTGAACTATAATCA
1 AAGTTTCATGTATA-A-TTGAACTA-AATCA
* *
32900750 AAGTTTCGTGTATAATTGCACTAAATCA
1 AAGTTTCATGTATAATTGAACTAAATCA
* *
32900778 AA-ATTCATGTATCATATTGTACATTAAATCA
1 AAGTTTCATGTAT-A-ATTG-A-ACTAAATCA
32900809 AAGTT
1 AAGTT
32900814 AAAGTATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
27 8 0.15
28 8 0.15
29 11 0.21
30 1 0.02
31 23 0.44
32 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (28 bp):
AAGTTTCATGTATAATTGAACTAAATCA
Found at i:32909827 original size:24 final size:26
Alignment explanation
Indices: 32909791--32909838 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
32909781 ATTCCAACTT
32909791 TCATATTTGTTTTT-C-ATATTTTAC
1 TCATATTTGTTTTTGCTATATTTTAC
32909815 TCAT-TTTGATTTTTGCTATATTTT
1 TCATATTTG-TTTTTGCTATATTTT
32909839 GTGGATTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 9 0.43
25 1 0.05
26 7 0.33
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (26 bp):
TCATATTTGTTTTTGCTATATTTTAC
Found at i:32914136 original size:37 final size:38
Alignment explanation
Indices: 32914066--32914137 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 38
32914056 AGTATTTAGA
* **
32914066 TTAATATATAAATATTATATATTACAATTTATAAATAT
1 TTAATATATAAATATTATATAGTACAAAATATAAATAT
* *
32914104 TTAATA-ATAAATATTTTATAGTATAAAATATAAA
1 TTAATATATAAATATTATATAGTACAAAATATAAA
32914138 CGTTTTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 23 0.79
38 6 0.21
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (38 bp):
TTAATATATAAATATTATATAGTACAAAATATAAATAT
Found at i:32922152 original size:21 final size:21
Alignment explanation
Indices: 32922119--32922158 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
32922109 ATCTCGAACT
*
32922119 CAAATCTTAAACCCTAAATCA
1 CAAACCTTAAACCCTAAATCA
* *
32922140 CAAACCTTGAACCTTAAAT
1 CAAACCTTAAACCCTAAAT
32922159 TAGTTTGGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.25
Consensus pattern (21 bp):
CAAACCTTAAACCCTAAATCA
Found at i:32940863 original size:40 final size:42
Alignment explanation
Indices: 32940775--32940860 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 42
32940765 AAATATTTTT
* *
32940775 AAACCCAAATATAATTTCATTATTCAAAAAACACTCATAAAC
1 AAACTCAAATATAATTTCATTACTCAAAAAACACTCATAAAC
* * *
32940817 TAAACTCAAATATAATTTTATTCCT-AAATAACACTCATAAAC
1 -AAACTCAAATATAATTTCATTACTCAAAAAACACTCATAAAC
32940859 AA
1 AA
32940861 CTCTTTTTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 2 0.05
42 16 0.42
43 20 0.53
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (42 bp):
AAACTCAAATATAATTTCATTACTCAAAAAACACTCATAAAC
Found at i:32941112 original size:18 final size:20
Alignment explanation
Indices: 32941081--32941118 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
32941071 TTTATTTGAC
32941081 TTTTATTGTGTTGTT-TTTA
1 TTTTATTGTGTTGTTGTTTA
*
32941100 TTTT-TTGTTTTGTTGTTTA
1 TTTTATTGTGTTGTTGTTTA
32941119 GAATGATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (20 bp):
TTTTATTGTGTTGTTGTTTA
Found at i:32946543 original size:29 final size:29
Alignment explanation
Indices: 32946489--32946546 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
32946479 TTATAGGGAC
* * *
32946489 TGGATCAAATTAGTCCTTCTATTATTAAA
1 TGGATCAAATTAGTCCCTATACTATTAAA
*
32946518 TGGATCAATTTAGTCCCTATACTATTAAA
1 TGGATCAAATTAGTCCCTATACTATTAAA
32946547 AAGAATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (29 bp):
TGGATCAAATTAGTCCCTATACTATTAAA
Found at i:32957914 original size:31 final size:32
Alignment explanation
Indices: 32957874--32957941 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 32
32957864 TTTTTGCTTC
* *
32957874 AATTAGGTACTTAAACTTGACTTATTGGTTCA
1 AATTAGGTACCTAAACTTGACTTATTGGTCCA
* * *
32957906 AATT-GGTACCTGAACTTGATTTTTTGGTCCA
1 AATTAGGTACCTAAACTTGACTTATTGGTCCA
32957937 AATTA
1 AATTA
32957942 ATATTTACGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (32 bp):
AATTAGGTACCTAAACTTGACTTATTGGTCCA
Found at i:32961852 original size:18 final size:16
Alignment explanation
Indices: 32961820--32961863 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
32961810 ATGAAATGAG
32961820 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
32961836 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
32961850 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
32961864 ATCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:32963276 original size:31 final size:32
Alignment explanation
Indices: 32963233--32963300 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 32
32963223 ATTTTAGAAT
*
32963233 TTTTTATATTTTAAATAGTTTTTTAAAATATA
1 TTTTTATATTTTAAAGAGTTTTTTAAAATATA
* *
32963265 TTTTTA-ATTTTAAAGAGTTTTTTCATATATA
1 TTTTTATATTTTAAAGAGTTTTTTAAAATATA
32963296 TTTTT
1 TTTTT
32963301 TAAAATATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (32 bp):
TTTTTATATTTTAAAGAGTTTTTTAAAATATA
Found at i:32963762 original size:21 final size:22
Alignment explanation
Indices: 32963737--32963783 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
32963727 TAACATTGAA
32963737 TTTT-AAA-AATTTTATTTATAT
1 TTTTAAAATAATTTT-TTTATAT
*
32963758 TTTTAAAATAATTTTTTTTTAT
1 TTTTAAAATAATTTTTTTATAT
32963780 TTTT
1 TTTT
32963784 TTTGAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 13 0.57
23 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTAAAATAATTTTTTTATAT
Found at i:32963844 original size:23 final size:23
Alignment explanation
Indices: 32963799--32963858 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 23
32963789 ATTTAAGGAG
32963799 TTTTTATTTTTTAAAAAATTATA-
1 TTTTTA-TTTTTAAAAAATTATAT
32963822 TTTTTATTTTT-AAAAATGATATAT
1 TTTTTATTTTTAAAAAAT--TATAT
32963846 TTTTTAATTTTTA
1 TTTTT-ATTTTTA
32963859 TGTTTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 6 0.19
22 5 0.16
23 10 0.31
24 5 0.16
25 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTTATTTTTAAAAAATTATAT
Found at i:32963848 original size:22 final size:23
Alignment explanation
Indices: 32963799--32963848 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 23
32963789 ATTTAAGGAG
*
32963799 TTTTTATTTTTTAAAAAATTATA
1 TTTTTATTTTTTAAAAAATGATA
32963822 TTTTTA-TTTTT-AAAAATGATA
1 TTTTTATTTTTTAAAAAATGATA
32963843 TATTTT
1 T-TTTT
32963849 TTAATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
23 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTTATTTTTTAAAAAATGATA
Found at i:32968362 original size:16 final size:16
Alignment explanation
Indices: 32968337--32968393 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
32968327 AAAATTTAAC
32968337 AAAAACTTAAAAAATAT
1 AAAAA-TTAAAAAATAT
32968354 AAAAATTAAAAAATA-
1 AAAAATTAAAAAATAT
*
32968369 ACTAAA-T-AAAAATAT
1 A-AAAATTAAAAAATAT
*
32968384 AAAGATTAAA
1 AAAAATTAAA
32968394 TCCATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.27
15 4 0.12
16 15 0.45
17 5 0.15
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (16 bp):
AAAAATTAAAAAATAT
Found at i:32968742 original size:16 final size:17
Alignment explanation
Indices: 32968721--32968757 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
32968711 CAAAAACAAT
*
32968721 AAAAATAA-TTATTTAC
1 AAAAATAATTTACTTAC
32968737 AAAAATAATTTACTTAC
1 AAAAATAATTTACTTAC
32968754 AAAA
1 AAAA
32968758 TTATGTACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATAATTTACTTAC
Found at i:32971703 original size:30 final size:30
Alignment explanation
Indices: 32971667--32971746 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
32971657 CAGTTTATCG
*
32971667 ATATGTGAAAGCCTTTGTGGCTATTCTGTT
1 ATATGTGAAAGCCTTTGTGGCTATTCTGAT
* * *
32971697 ATATGTGAAAGCCTTTGTCGTTGTTCTGAT
1 ATATGTGAAAGCCTTTGTGGCTATTCTGAT
32971727 ATATGT-ATAAGCCTTTGTGG
1 ATATGTGA-AAGCCTTTGTGG
32971747 TGAAACCTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 1 0.02
30 43 0.98
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (30 bp):
ATATGTGAAAGCCTTTGTGGCTATTCTGAT
Found at i:32971992 original size:30 final size:30
Alignment explanation
Indices: 32971956--32972036 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
32971946 CAGTTTACCA
* *
32971956 ATATGTGAAAGCCTTTATGGCTATTCTGTT
1 ATATGTGAAAGCCTTTGTGGCTATTCTGAT
* * *
32971986 ATATGTGAAAGCCTTTGTCGTTGTTCTGAT
1 ATATGTGAAAGCCTTTGTGGCTATTCTGAT
32972016 ATATGT-ATAAGCCTTTGTGGC
1 ATATGTGA-AAGCCTTTGTGGC
32972037 AAAACCTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 1 0.02
30 42 0.98
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (30 bp):
ATATGTGAAAGCCTTTGTGGCTATTCTGAT
Found at i:32972013 original size:289 final size:289
Alignment explanation
Indices: 32971494--32972074 Score: 1027
Period size: 289 Copynumber: 2.0 Consensus size: 289
32971484 CCTAGTTGTA
*
32971494 TTGCTATGGCATCATATGGCAAATGAAAACCACATCATGTAAGACCTAGCTTGGGACTACGGCGT
1 TTGCTATGGCATCATATGGCAAATGAAAACCACATCATGTAAGACCTAGCTTGGGACTACGACGT
*
32971559 CATGTGGAGATATATAAAGGACGATTTGGTGAGTACCAGGCAATGAGGGACAAACCTCATGATGA
66 CAAGTGGAGATATATAAAGGACGATTTGGTGAGTACCAGGCAATGAGGGACAAACCTCATGATGA
* * * * *
32971624 TAAGTTTAGGTGAATCCTTATCATTGAAAACACCAGTTTATCGATATGTGAAAGCCTTTGTGGCT
131 TAAGTTTAGGTGAATCCCTATCATTAAAAACACCAGTTTACCAATATGTGAAAGCCTTTATGGCT
**
32971689 ATTCTGTTATATGTGAAAGCCTTTGTCGTTGTTCTGATATATGTATAAGCCTTTGTGGTGAAACC
196 ATTCTGTTATATGTGAAAGCCTTTGTCGTTGTTCTGATATATGTATAAGCCTTTGTGGCAAAACC
* *
32971754 TAGTATATGTGAGCATTTATGGCTTTTCT
261 TAGTATATGTGAGCATTTATGACTATTCT
*
32971783 TTGCTATGGCATCATATGGCAAATGAAAACCACATTATGTAAGACCTAGCTTGGGACTACGACGT
1 TTGCTATGGCATCATATGGCAAATGAAAACCACATCATGTAAGACCTAGCTTGGGACTACGACGT
* *
32971848 CAAGTGGAGATATATAAAGGACGATTTGGTGAGTACCGGGCAATGAGGGATAAACCTCATGATGA
66 CAAGTGGAGATATATAAAGGACGATTTGGTGAGTACCAGGCAATGAGGGACAAACCTCATGATGA
32971913 TAAGTTTAGGTGAATCCCTATCATTAAAAACACCAGTTTACCAATATGTGAAAGCCTTTATGGCT
131 TAAGTTTAGGTGAATCCCTATCATTAAAAACACCAGTTTACCAATATGTGAAAGCCTTTATGGCT
32971978 ATTCTGTTATATGTGAAAGCCTTTGTCGTTGTTCTGATATATGTATAAGCCTTTGTGGCAAAACC
196 ATTCTGTTATATGTGAAAGCCTTTGTCGTTGTTCTGATATATGTATAAGCCTTTGTGGCAAAACC
*
32972043 TAGTATATGTGAGCATTTGTGACTATTCT
261 TAGTATATGTGAGCATTTATGACTATTCT
32972072 TTG
1 TTG
32972075 TTATATGTGA
Statistics
Matches: 277, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
289 277 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (289 bp):
TTGCTATGGCATCATATGGCAAATGAAAACCACATCATGTAAGACCTAGCTTGGGACTACGACGT
CAAGTGGAGATATATAAAGGACGATTTGGTGAGTACCAGGCAATGAGGGACAAACCTCATGATGA
TAAGTTTAGGTGAATCCCTATCATTAAAAACACCAGTTTACCAATATGTGAAAGCCTTTATGGCT
ATTCTGTTATATGTGAAAGCCTTTGTCGTTGTTCTGATATATGTATAAGCCTTTGTGGCAAAACC
TAGTATATGTGAGCATTTATGACTATTCT
Found at i:32972115 original size:29 final size:29
Alignment explanation
Indices: 32972025--32972141 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
32972015 TATATGTATA
*
32972025 AGCCTTTGTGGCAAAACCTAG-TATATGTG
1 AGCCTTTGTGGCGAAACCT-GTTATATGTG
* * * ** *
32972054 AGCATTTGTGACTATTCTTTGTTATATGTG
1 AGCCTTTGTGGCGAAAC-CTGTTATATGTG
32972084 AGCCTTTGTGGCGAAACCTGTTATATGTG
1 AGCCTTTGTGGCGAAACCTGTTATATGTG
* *
32972113 AGCCCTTGTGGCGAAACTTGTTATATGTG
1 AGCCTTTGTGGCGAAACCTGTTATATGTG
32972142 GAAACACTTG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
29 51 0.71
30 21 0.29
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (29 bp):
AGCCTTTGTGGCGAAACCTGTTATATGTG
Found at i:32972155 original size:31 final size:29
Alignment explanation
Indices: 32972073--32972155 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
32972063 GACTATTCTT
*
32972073 TGTTATATGTGAGC-CTTTGTGGCGAAACC
1 TGTTATATGTGAACAC-TTGTGGCGAAACC
* * *
32972102 TGTTATATGTGAGCCCTTGTGGCGAAACT
1 TGTTATATGTGAACACTTGTGGCGAAACC
32972131 TGTTATATGTGGAAACACTTGTGGC
1 TGTTATATGT-G-AACACTTGTGGC
32972156 TGTCCTTTGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
29 36 0.75
30 2 0.04
31 10 0.21
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.35
Consensus pattern (29 bp):
TGTTATATGTGAACACTTGTGGCGAAACC
Found at i:32981513 original size:22 final size:22
Alignment explanation
Indices: 32981469--32981518 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
32981459 AATATTTAAA
* **
32981469 ATTT-AAAATTTTAATTTTTTT
1 ATTTGAAAATATTAATTTAATT
32981490 ATTTGAAAATATTAATTTAATT
1 ATTTGAAAATATTAATTTAATT
32981512 A-TTGAAA
1 ATTTGAAA
32981519 TTATAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
ATTTGAAAATATTAATTTAATT
Found at i:32988143 original size:30 final size:29
Alignment explanation
Indices: 32988109--32988168 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
32988099 AATTGAATAG
32988109 TGAAGTAACCATTTTATAAT-TTTTCATAAT
1 TGAAG-AACCATTTTA-AATCTTTTCATAAT
* * *
32988139 TGAAGGACTATTTTACATCTTTTCATAAT
1 TGAAGAACCATTTTAAATCTTTTCATAAT
32988168 T
1 T
32988169 ATCGGAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 2 0.08
29 19 0.73
30 5 0.19
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (29 bp):
TGAAGAACCATTTTAAATCTTTTCATAAT
Found at i:32989349 original size:17 final size:17
Alignment explanation
Indices: 32989327--32989442 Score: 155
Period size: 17 Copynumber: 6.8 Consensus size: 17
32989317 AACTTTTAAT
32989327 TTTTAAATCTT-AATTTA
1 TTTTAAAT-TTAAATTTA
32989344 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
32989361 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
32989378 TTTTAAATTTAAATTCA
1 TTTTAAATTTAAATTTA
32989395 -TTTAGAATTTAAATTTA
1 TTTTA-AATTTAAATTTA
* *
32989412 TGTTAAATTTGAATTTA
1 TTTTAAATTTAAATTTA
* *
32989429 TTTTGAATTAAAAT
1 TTTTAAATTTAAAT
32989443 AATTTAAATA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
16 6 0.07
17 79 0.90
18 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:32989354 original size:11 final size:11
Alignment explanation
Indices: 32989338--32989428 Score: 62
Period size: 11 Copynumber: 8.0 Consensus size: 11
32989328 TTTAAATCTT
*
32989338 AATTTATTTTA
1 AATTTAATTTA
32989349 AATTTAAATTT-
1 AATTT-AATTTA
*
32989360 ATTTTAAATTTA
1 AATTT-AATTTA
*
32989372 AATTTATTTTA
1 AATTTAATTTA
*
32989383 AATTTAAATT-
1 AATTTAATTTA
*
32989393 CATTTAGAATTTA
1 AATTT--AATTTA
32989406 AATTT-ATGTTA
1 AATTTAAT-TTA
32989417 AATTTGAATTTA
1 AATTT-AATTTA
32989429 TTTTGAATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
10 6 0.10
11 36 0.57
12 15 0.24
13 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:32989356 original size:23 final size:23
Alignment explanation
Indices: 32989329--32989428 Score: 75
Period size: 23 Copynumber: 4.4 Consensus size: 23
32989319 CTTTTAATTT
*
32989329 TTAAATCTT-AATTTATTTTAAAT
1 TTAAAT-TTAAATTTAATTTAAAT
*
32989352 TTAAATTT-ATTTTAAATTTAAAT
1 TTAAATTTAAATTT-AATTTAAAT
* * *
32989375 TT-ATTTTAAATTTAAATT-CAT
1 TTAAATTTAAATTTAATTTAAAT
32989396 TTAGAATTTAAATTT-ATGTTAAAT
1 TTA-AATTTAAATTTAAT-TTAAAT
*
32989420 TTGAATTTA
1 TTAAATTTA
32989429 TTTTGAATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
21 4 0.07
22 15 0.25
23 38 0.62
24 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (23 bp):
TTAAATTTAAATTTAATTTAAAT
Found at i:32989404 original size:7 final size:6
Alignment explanation
Indices: 32989328--32989428 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
32989318 ACTTTTAATT
* *
32989328 TTTAAA TCTT-AA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
32989374 TTT-AT TTTAAA TTTAAA -TT-CA TTTAGAA TTTAAA TTT--A TGTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA T-TTAAA
*
32989419 TTTGAA TTTA
1 TTTAAA TTTA
32989429 TTTTGAATTA
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
4 3 0.04
5 20 0.27
6 43 0.57
7 9 0.12
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:32991484 original size:30 final size:30
Alignment explanation
Indices: 32991450--32991703 Score: 130
Period size: 30 Copynumber: 8.6 Consensus size: 30
32991440 AACTGTCTAG
* * *
32991450 AAATTATATTTTAACCCCTAAACTTCTTCA
1 AAATTACATTTTAACCCCAAAACTTCTCCA
* *
32991480 AAATTACATTTTGACCCCAAAATTTCTCCA
1 AAATTACATTTTAACCCCAAAACTTCTCCA
** ** *
32991510 AAATTACA-TCAAACCTAAAAACTTC-CAA
1 AAATTACATTTTAACCCCAAAACTTCTCCA
* ** * *
32991538 AAATTACATTTTTTACCCCCGAACAT-TCAA
1 AAATTACA-TTTTAACCCCAAAACTTCTCCA
* * *
32991568 AAATTCCATTTTTGACCCAAAAACTTCT-CA
1 AAATTACA-TTTTAACCCCAAAACTTCTCCA
* * * **
32991598 AAATTACGTTTTTACCCCCAAACTTC-AAA
1 AAATTACATTTTAACCCCAAAACTTCTCCA
* * **
32991627 AAATTCCATTTTTAACCTCAAAACTTC-AAA
1 AAATTACA-TTTTAACCCCAAAACTTCTCCA
* * *
32991657 AAATTATATTTTTGACCCCAAAAC-TCT-TA
1 AAATTACA-TTTTAACCCCAAAACTTCTCCA
32991686 AAATTACCATTTT-ACCCC
1 AAATTA-CATTTTAACCCC
32991704 TGGATGTTCA
Statistics
Matches: 172, Mismatches: 44, Indels: 18
0.74 0.19 0.08
Matches are distributed among these distances:
28 15 0.09
29 46 0.27
30 110 0.64
31 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATTACATTTTAACCCCAAAACTTCTCCA
Found at i:32991580 original size:29 final size:29
Alignment explanation
Indices: 32991528--32991703 Score: 142
Period size: 30 Copynumber: 6.0 Consensus size: 29
32991518 TCAAACCTAA
*
32991528 AAACTTCCAAAAATTACATTTTTTACCCCC
1 AAACTTCAAAAAATTACA-TTTTTACCCCC
* * **
32991558 GAACATTC-AAAAATTCCATTTTTGACCCAA
1 AAAC-TTCAAAAAATTACATTTTT-ACCCCC
** *
32991588 AAACTTCTCAAAATTACGTTTTTACCCCC
1 AAACTTCAAAAAATTACATTTTTACCCCC
* * *
32991617 AAACTTCAAAAAATTCCATTTTTAACCTCA
1 AAACTTCAAAAAATTACATTTTT-ACCCCC
* *
32991647 AAACTTCAAAAAATTATATTTTTGACCCCA
1 AAACTTCAAAAAATTACATTTTT-ACCCCC
**
32991677 AAAC-TCTTAAAATTACCA-TTTTACCCC
1 AAACTTCAAAAAATTA-CATTTTTACCCC
32991704 TGGATGTTCA
Statistics
Matches: 118, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
28 5 0.04
29 44 0.37
30 66 0.56
31 3 0.03
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (29 bp):
AAACTTCAAAAAATTACATTTTTACCCCC
Found at i:32991635 original size:59 final size:58
Alignment explanation
Indices: 32991521--32991698 Score: 184
Period size: 59 Copynumber: 3.0 Consensus size: 58
32991511 AATTACATCA
*
32991521 AACCT-AAAAACTTCCAAAAATTACATTTTTTACCCCCGAACATTCAAAAATTCCATTTTT
1 AACCTCAAAAACTTCC-AAAATTACA-TTTTTACCCCCAAAC-TTCAAAAATTCCATTTTT
* *
32991581 GACC-CAAAAACTTCTCAAAATTACGTTTTTACCCCCAAACTTCAAAAAATTCCATTTTT
1 AACCTCAAAAACTTC-CAAAATTACATTTTTACCCCCAAACTTC-AAAAATTCCATTTTT
* * * *
32991640 AACCTC-AAAACTTCAAAAAATTATATTTTTGACCCCAAAAC-TCTTAAAATTACCATTTT
1 AACCTCAAAAACTTC-CAAAATTACATTTTT-ACCCCCAAACTTC-AAAAATT-CCATTTT
32991699 ACCCCTGGAT
Statistics
Matches: 101, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
58 3 0.03
59 60 0.59
60 37 0.37
61 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (58 bp):
AACCTCAAAAACTTCCAAAATTACATTTTTACCCCCAAACTTCAAAAATTCCATTTTT
Found at i:32991699 original size:59 final size:61
Alignment explanation
Indices: 32991479--32991698 Score: 181
Period size: 59 Copynumber: 3.7 Consensus size: 61
32991469 AAACTTCTTC
** * * ** * *
32991479 AAAATTACA-TTTTGACCCCAAAATTTCTCCAAAATTACA--TCAAACCTAAAAACTTCCA
1 AAAATTACATTTTTGACCCCAAAACATCTCAAAAATTCCATTTTTAACCTCAAAACTTCAA
* ** * **
32991537 AAAATTACATTTTTTACCCCCGAACAT-TCAAAAATTCCATTTTTGACC-CAAAAACTTCTC
1 AAAATTACATTTTTGACCCCAAAACATCTCAAAAATTCCATTTTTAACCTC-AAAACTTCAA
* *
32991597 AAAATTACGTTTTT-ACCCCCAAAC-T-TCAAAAAATTCCATTTTTAACCTCAAAACTTCAA
1 AAAATTACATTTTTGACCCCAAAACATCTC-AAAAATTCCATTTTTAACCTCAAAACTTCAA
* *
32991656 AAAATTATATTTTTGACCCCAAAAC-TCT-TAAAATTACCATTTT
1 AAAATTACATTTTTGACCCCAAAACATCTCAAAAATT-CCATTTT
32991699 ACCCCTGGAT
Statistics
Matches: 131, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
58 22 0.17
59 65 0.50
60 43 0.33
61 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.33
Consensus pattern (61 bp):
AAAATTACATTTTTGACCCCAAAACATCTCAAAAATTCCATTTTTAACCTCAAAACTTCAA
Found at i:32991852 original size:28 final size:28
Alignment explanation
Indices: 32991799--32991861 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
32991789 TCAAATTTTT
*
32991799 TCCAAAATTACCATTTTGCTCCCGAG-A
1 TCCAAAATTACCATTTTACTCCCGAGCA
32991826 GTCCAAAATTACCATTTTAC-CCTCGAGCA
1 -TCCAAAATTACCATTTTACTCC-CGAGCA
32991855 TCCAAAA
1 TCCAAAA
32991862 AGTCTCGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 2 0.06
28 29 0.91
29 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACTCCCGAGCA
Found at i:32991979 original size:28 final size:28
Alignment explanation
Indices: 32991947--32992008 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
32991937 TAAAGTTTTC
*
32991947 CCAAAATTACCATTTTACCCTCGAG-AGT
1 CCAAAATTACCATTTTACCCCCGAGCA-T
*
32991975 CCAAAATTACCATTTTGCCCCCGAGCAT
1 CCAAAATTACCATTTTACCCCCGAGCAT
32992003 CCAAAA
1 CCAAAA
32992009 AGCCCCCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGCAT
Found at i:32992126 original size:146 final size:142
Alignment explanation
Indices: 32991723--32992114 Score: 396
Period size: 147 Copynumber: 2.7 Consensus size: 142
32991713 AAAAATCTCA
* * * * * **
32991723 TTTTGATCCCGATTTTTTTAAAAATTATAGTTTTACCCTCGATTGTCTAAAATGTTGTTTTTAAC
1 TTTTGATCCCGATTCTTTCAAAAATTACA-TTTTACCCTC-AATGACTAAAATGTCATTTTTAAC
* *
32991788 CTCAAATTTTTTCCAAAATTACCATTTTGCTCC-CGAGAGTCCAAAATTACCATTTTACCCTCGA
64 C-CAAA-TTTTTCCAAAATTACCATTTTAC-CCTCGAGAGTCCAAAATTACCATTTTACCCCCGA
* * *
32991852 GCATCCAAAAAGTCTCG
126 GCATCCAAAAAGCCCCC
** * * * * *
32991869 TTTTTTTCTCTCGATTC-TTCTGAAAATTATCGTTTTACCCCCGAA-CATCTAAAATGTCATTTC
1 TTTTGATC-C-CGATTCTTTC-AAAAATTA-CATTTTACCCTC-AATGA-CTAAAATGTCATTTT
* * *
32991932 TAACCTAAAGTTTTCCCAAAATTACCATTTTACCCTCGAGAGTCCAAAATTACCATTTTGCCCCC
60 TAACCCAAA-TTTTTCCAAAATTACCATTTTACCCTCGAGAGTCCAAAATTACCATTTTACCCCC
32991997 GAGCATCCAAAAAGCCCCC
124 GAGCATCCAAAAAGCCCCC
*
32992016 TTCTTGATCCCGATTCTTTCAAAAATTACCATTTTACCCTTAAGTGACTAAAATGTCATTTTTAA
1 TT-TTGATCCCGATTCTTTCAAAAATTA-CATTTTACCCTCAA-TGACTAAAATGTCATTTTTAA
32992081 CTCCAAA-TTTTCCTAAAATTACCATTTTACCCTC
63 C-CCAAATTTTTCC-AAAATTACCATTTTACCCTC
32992115 AAGCATCCAA
Statistics
Matches: 200, Mismatches: 34, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
145 7 0.04
146 68 0.34
147 81 0.41
148 44 0.22
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (142 bp):
TTTTGATCCCGATTCTTTCAAAAATTACATTTTACCCTCAATGACTAAAATGTCATTTTTAACCC
AAATTTTTCCAAAATTACCATTTTACCCTCGAGAGTCCAAAATTACCATTTTACCCCCGAGCATC
CAAAAAGCCCCC
Found at i:32992165 original size:117 final size:118
Alignment explanation
Indices: 32991975--32992243 Score: 425
Period size: 117 Copynumber: 2.3 Consensus size: 118
32991965 CCTCGAGAGT
* * *
32991975 CCAAAATTACCATTTTGCCCCCGAGCATCCAAAAAGCCCCCTTCTTGATCCCGATTCTTTCAAAA
1 CCAAAATTACCATTTTACCCCCAAGCATCCAAAAAGCCCCATTCTTGATCCCGATTCTTTCAAAA
*
32992040 ATTACCATTTTACCCTTAAGTGACTAAAATGTCATTTTTAACTCCAAATTTTC
66 ATTACCATTTTACCCTTAAGTGACTAAAATGTCATTTTTAACCCCAAATTTTC
* * * *
32992093 CTAAAATTACCATTTTACCCTCAAGCATCCAAAAAGTCCCATT-TTTATCCCGATTCTTTCAAAA
1 CCAAAATTACCATTTTACCCCCAAGCATCCAAAAAGCCCCATTCTTGATCCCGATTCTTTCAAAA
*
32992157 ATTACCATTTTACCCTTAAGTGTCTAAAATGTCATTTTTAACCCCAAATTTTC
66 ATTACCATTTTACCCTTAAGTGACTAAAATGTCATTTTTAACCCCAAATTTTC
*
32992210 CCAAAATTACCATTTTACCCCGAAG-AGTCCAAAA
1 CCAAAATTACCATTTTACCCCCAAGCA-TCCAAAA
32992244 TTACCATTTT
Statistics
Matches: 138, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
116 1 0.01
117 100 0.72
118 37 0.27
ACGTcount: A:0.33, C:0.28, G:0.07, T:0.33
Consensus pattern (118 bp):
CCAAAATTACCATTTTACCCCCAAGCATCCAAAAAGCCCCATTCTTGATCCCGATTCTTTCAAAA
ATTACCATTTTACCCTTAAGTGACTAAAATGTCATTTTTAACCCCAAATTTTC
Found at i:32992171 original size:59 final size:59
Alignment explanation
Indices: 32991977--32992172 Score: 202
Period size: 58 Copynumber: 3.3 Consensus size: 59
32991967 TCGAGAGTCC
* * * * * *
32991977 AAAATTACCATTTTGCCCCCGAGCATCCAAAAAGCCCCCTTCTTGATCCCGATTCTTTCA
1 AAAATTACCATTTTACCCTCAAGCATCCAAAAAGTCCCATT-TTTATCCCGATTCTTTCA
* * * * ** * *
32992037 AAAATTACCATTTTACCCTTAAGTGA-CTAAAATGT--CATTTTTAACTCCAAATT-TTCCT
1 AAAATTACCATTTTACCCTCAAG-CATCCAAAAAGTCCCATTTTT-A-TCCCGATTCTTTCA
32992095 AAAATTACCATTTTACCCTCAAGCATCCAAAAAGTCCCATTTTTATCCCGATTCTTTCA
1 AAAATTACCATTTTACCCTCAAGCATCCAAAAAGTCCCATTTTTATCCCGATTCTTTCA
32992154 AAAATTACCATTTTACCCT
1 AAAATTACCATTTTACCCT
32992173 TAAGTGTCTA
Statistics
Matches: 107, Mismatches: 22, Indels: 15
0.74 0.15 0.10
Matches are distributed among these distances:
57 3 0.03
58 42 0.39
59 29 0.27
60 32 0.30
61 1 0.01
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAGCATCCAAAAAGTCCCATTTTTATCCCGATTCTTTCA
Found at i:32992215 original size:59 final size:58
Alignment explanation
Indices: 32992035--32992229 Score: 241
Period size: 58 Copynumber: 3.3 Consensus size: 58
32992025 CCGATTCTTT
* *
32992035 CAAAAATTACCATTTTACCCTTAAGTGACTAAAATGTCATTTTTAACTCCAAATTTTC
1 CAAAAATTACCATTTTACCCTTAAGTGTCTAAAATGTCATTTTTAACCCCAAATTTTC
* * ** * * * * *
32992093 CTAAAATTACCATTTTACCCTCAAGCATCCAAAAAGTCCCATTTTT-ATCCC-GATTCTTT
1 CAAAAATTACCATTTTACCCTTAAGTGTCTAAAATGT--CATTTTTAACCCCAAATT-TTC
32992152 CAAAAATTACCATTTTACCCTTAAGTGTCTAAAATGTCATTTTTAACCCCAAATTTTC
1 CAAAAATTACCATTTTACCCTTAAGTGTCTAAAATGTCATTTTTAACCCCAAATTTTC
*
32992210 CCAAAATTACCATTTTACCC
1 CAAAAATTACCATTTTACCC
32992230 CGAAGAGTCC
Statistics
Matches: 111, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
57 7 0.06
58 58 0.52
59 39 0.35
60 7 0.06
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCTTAAGTGTCTAAAATGTCATTTTTAACCCCAAATTTTC
Found at i:32996744 original size:8 final size:8
Alignment explanation
Indices: 32996727--32996761 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
32996717 TGTGATTAGA
*
32996727 TTAAAATT
1 TTAAATTT
32996735 TTAAATTT
1 TTAAATTT
32996743 TTAAATTT
1 TTAAATTT
32996751 TTAAATTT
1 TTAAATTT
32996759 TTA
1 TTA
32996762 GAGAGAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAAATTT
Found at i:32997660 original size:19 final size:19
Alignment explanation
Indices: 32997636--32997691 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
32997626 TATTTTAAAG
32997636 TTAAATATTATAATTATTT
1 TTAAATATTATAATTATTT
* **
32997655 TTAAATA-TAAAATT-TAG
1 TTAAATATTATAATTATTT
32997672 TTAAATATTATAA-TATTT
1 TTAAATATTATAATTATTT
32997690 TT
1 TT
32997692 TTCAAATTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 9 0.31
18 13 0.45
19 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTAAATATTATAATTATTT
Found at i:33010344 original size:3 final size:3
Alignment explanation
Indices: 33010336--33010403 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
33010326 AGTCTACTAT
* * *
33010336 ATG ATG ATG ATG ATG TTG ATA AGG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
33010384 ATG ATG ATG ATG GTG ATG AT
1 ATG ATG ATG ATG ATG ATG AT
33010404 AATAAAATGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:33010797 original size:15 final size:17
Alignment explanation
Indices: 33010758--33010802 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
33010748 GTTTCATATA
33010758 GGAAGAGAAAAAACCAGT
1 GGAAGAGAAAAAA-CAGT
*
33010776 TGAAGAGAAAAAA-A-T
1 GGAAGAGAAAAAACAGT
33010791 GGAAGAGAAAAA
1 GGAAGAGAAAAA
33010803 GGTTGGAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
18 12 0.48
ACGTcount: A:0.62, C:0.04, G:0.27, T:0.07
Consensus pattern (17 bp):
GGAAGAGAAAAAACAGT
Found at i:33020652 original size:13 final size:14
Alignment explanation
Indices: 33020634--33020665 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
33020624 ATAGGAGATG
33020634 AATTAATTA-AATT
1 AATTAATTACAATT
33020647 AATTAATTACAATT
1 AATTAATTACAATT
33020661 -ATTAA
1 AATTAA
33020666 GAAAGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAATTACAATT
Found at i:33022996 original size:4 final size:4
Alignment explanation
Indices: 33022987--33023013 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
33022977 TATACATATG
33022987 GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTA
33023014 CAATTCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:33024223 original size:29 final size:30
Alignment explanation
Indices: 33024191--33024249 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
33024181 TCACGTGTAT
*
33024191 AATTGCAC-CAAATCAAAGTTCATGTATAC
1 AATTACACACAAATCAAAGTTCATGTATAC
*
33024220 AATTACACATTAAATCAAAGTTCATGTATA
1 AATTACACA-CAAATCAAAGTTCATGTATA
33024250 ATTTTGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
31 19 0.73
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (30 bp):
AATTACACACAAATCAAAGTTCATGTATAC
Found at i:33028024 original size:78 final size:79
Alignment explanation
Indices: 33027881--33028027 Score: 201
Period size: 78 Copynumber: 1.9 Consensus size: 79
33027871 TTTTAAAAGG
* * *
33027881 ATTAAAGTATAATTTTACTATATATTAATTTATAATTTATTTATTTATAAAAGGATTGAAATTAA
1 ATTAAAGTAGAATTTCAC-ATATATTAATTTATAATTTATTTATTTATAAAAGGACTGAAATTAA
33027946 AAAAAATATTTTGAA
65 AAAAAATATTTTGAA
* *
33027961 ATTAAAGTAGAATTTCAC-TATATTAATTTATATTTTTATTTATTTATAAGAA-TACTG-AATTA
1 ATTAAAGTAGAATTTCACATATATTAATTTATA-ATTTATTTATTTATAA-AAGGACTGAAATTA
33028023 AAAAA
64 AAAAA
33028028 TTTCTTTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
78 24 0.40
79 18 0.30
80 18 0.30
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (79 bp):
ATTAAAGTAGAATTTCACATATATTAATTTATAATTTATTTATTTATAAAAGGACTGAAATTAAA
AAAAATATTTTGAA
Found at i:33031801 original size:23 final size:23
Alignment explanation
Indices: 33031774--33031820 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
33031764 TAAAATTGAT
33031774 AATTTAATTGAGTGAATTAATTA
1 AATTTAATTGAGTGAATTAATTA
* * * *
33031797 AATTTATTTTAGTTAATTATTTA
1 AATTTAATTGAGTGAATTAATTA
33031820 A
1 A
33031821 TGAGTAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
AATTTAATTGAGTGAATTAATTA
Found at i:33032135 original size:18 final size:19
Alignment explanation
Indices: 33032108--33032143 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
33032098 TTTTATATAT
33032108 TTTTATATTTTTTAAAAAA
1 TTTTATATTTTTTAAAAAA
33032127 TTTTA-ATTTTTTAAAAA
1 TTTTATATTTTTTAAAAA
33032144 TACAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATATTTTTTAAAAAA
Found at i:33032177 original size:19 final size:18
Alignment explanation
Indices: 33032150--33032214 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
33032140 AAAATACAAA
*
33032150 ATTTAGAATTTTTATAAAT
1 ATTTTGAATTTTTA-AAAT
33032169 ATTTTGAA-TTTTAACAATT
1 ATTTTGAATTTTTAA-AA-T
*
33032188 ATTTTCAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAA-T
33032208 ATTTTGA
1 ATTTTGA
33032215 TTATTTTGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 15 0.38
20 14 0.36
21 2 0.05
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (18 bp):
ATTTTGAATTTTTAAAAT
Found at i:33032207 original size:20 final size:19
Alignment explanation
Indices: 33032156--33032212 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
33032146 CAAAATTTAG
*
33032156 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTC
33032175 AA-TTTTAACAATTATTTTC
1 AATTTTTAA-AATTATTTTC
33032194 AATTTTTGAAAATTATTTT
1 AATTTTT-AAAATTATTTT
33032213 GATTATTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 10 0.30
20 13 0.39
21 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTC
Found at i:33032426 original size:16 final size:15
Alignment explanation
Indices: 33032388--33032426 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
33032378 TGATTCGAAT
*
33032388 AATTCGAATAACTCA
1 AATTCGATTAACTCA
33032403 AA-TCGATTAACTCAA
1 AATTCGATTAACTC-A
33032418 AATTCGATT
1 AATTCGATT
33032427 TTTTATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 10 0.48
15 5 0.24
16 6 0.29
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.31
Consensus pattern (15 bp):
AATTCGATTAACTCA
Found at i:33039455 original size:19 final size:19
Alignment explanation
Indices: 33039418--33039457 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
33039408 TAAAGTTGGC
*
33039418 TCAATGGTTTTTATCCGAT
1 TCAATGGTTTGTATCCGAT
33039437 TCAATCGGTTTGTAT-CGAT
1 TCAAT-GGTTTGTATCCGAT
33039456 TC
1 TC
33039458 TTAAATCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.45
Consensus pattern (19 bp):
TCAATGGTTTGTATCCGAT
Found at i:33062325 original size:3 final size:3
Alignment explanation
Indices: 33062312--33062356 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
33062302 GAGAAAGAGA
* *
33062312 AAG AGG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AGG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
33062357 TGGAAGAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33062361 original size:6 final size:6
Alignment explanation
Indices: 33062299--33062391 Score: 66
Period size: 6 Copynumber: 16.0 Consensus size: 6
33062289 AATGGAAGTT
* * * * * * *
33062299 GAAGAG AAAGAG AAAGAG GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
* * * *
33062347 GAAGAG GAAGTG GAAGA- GAAG-G G-GGAG GAGGAG GAAGAA GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
33062392 AGTGAAGATG
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
4 1 0.01
5 7 0.09
6 66 0.89
ACGTcount: A:0.55, C:0.00, G:0.44, T:0.01
Consensus pattern (6 bp):
GAAGAG
Found at i:33066925 original size:18 final size:18
Alignment explanation
Indices: 33066902--33066940 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
33066892 AGTGAGGAGA
* *
33066902 ATGCTGATACAGGTGGTG
1 ATGCTGATAAAGATGGTG
33066920 ATGCTGATAAAGATGGTG
1 ATGCTGATAAAGATGGTG
33066938 ATG
1 ATG
33066941 GAGATGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (18 bp):
ATGCTGATAAAGATGGTG
Found at i:33076602 original size:2 final size:2
Alignment explanation
Indices: 33076595--33076626 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33076585 AGCTCTATTT
33076595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33076627 CACACACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33077668 original size:12 final size:13
Alignment explanation
Indices: 33077638--33077673 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
33077628 TTAATAATTG
33077638 AAATATTGTAAATA
1 AAATATT-TAAATA
33077652 AAATATTTAAA-A
1 AAATATTTAAATA
33077664 AAATATTTAA
1 AAATATTTAA
33077674 TGTATTATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 4 0.18
14 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (13 bp):
AAATATTTAAATA
Found at i:33084277 original size:53 final size:53
Alignment explanation
Indices: 33084165--33084464 Score: 393
Period size: 53 Copynumber: 5.6 Consensus size: 53
33084155 TTCACATTTG
* *
33084165 ATAACTCAAGATGACACAGAGTCATCAGACCTTTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACC-TTTAATCCGTAATAGGATTCAT
*
33084219 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTTAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * * * *
33084272 ATAACTCACGACGACATACAGTCATCGGACCTTTAATTCATAATAGGATTCAC
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * * * *
33084325 ATAACTTATGATGAAACAGAGTCATCGAACCTTTAATCTGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * ** *
33084378 ATAACTCACGATGACACAAAGTAATTTGACATTTAATCCGTAATAGGATTCAT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
* * *
33084431 ATAACTCAAGATGACATAAAGTCATCGGACCTTT
1 ATAACTCACGATGACACAGAGTCATCGGACCTTT
33084465 TTGTATTTAT
Statistics
Matches: 209, Mismatches: 37, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
53 180 0.86
54 29 0.14
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (53 bp):
ATAACTCACGATGACACAGAGTCATCGGACCTTTAATCCGTAATAGGATTCAT
Found at i:33089931 original size:14 final size:16
Alignment explanation
Indices: 33089900--33089932 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
33089890 TACAAAAAAT
33089900 ATAAATATTTTTATAA
1 ATAAATATTTTTATAA
33089916 ATAAAT-TTTTTA-AA
1 ATAAATATTTTTATAA
33089930 ATA
1 ATA
33089933 TATTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 6 0.35
16 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAAATATTTTTATAA
Found at i:33091815 original size:4 final size:4
Alignment explanation
Indices: 33091806--33091833 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
33091796 TGTCTAACCG
33091806 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT
33091834 CAGTTATTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:33099140 original size:13 final size:13
Alignment explanation
Indices: 33099122--33099146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33099112 ATTTTAAAGC
33099122 TAATTAATATATT
1 TAATTAATATATT
33099135 TAATTAATATAT
1 TAATTAATATAT
33099147 AGTATAGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAATTAATATATT
Found at i:33108377 original size:19 final size:19
Alignment explanation
Indices: 33108355--33108401 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
33108345 ATATATTTTT
*
33108355 AAAATATATAATACA-TAAA
1 AAAATATA-AAAACATTAAA
33108374 AAAATACTAAAAACATTAAA
1 AAAATA-TAAAAACATTAAA
33108394 ATAAATAT
1 A-AAATAT
33108402 TTCCCAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 11 0.46
20 8 0.33
21 5 0.21
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAATATAAAAACATTAAA
Found at i:33108554 original size:25 final size:25
Alignment explanation
Indices: 33108489--33108554 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
33108479 ATGCCTCTAA
33108489 AATAGTAACAAAATTAACAATAAAAT
1 AATAGTAACAAAA-TAACAATAAAAT
* * * *
33108515 AAGAGTTATACAATAACAATAAAAT
1 AATAGTAACAAAATAACAATAAAAT
* *
33108540 AATAGCAACATAATA
1 AATAGTAACAAAATA
33108555 GTGAAATAGT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
25 22 0.71
26 9 0.29
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.23
Consensus pattern (25 bp):
AATAGTAACAAAATAACAATAAAAT
Found at i:33109100 original size:79 final size:79
Alignment explanation
Indices: 33108964--33109840 Score: 529
Period size: 79 Copynumber: 11.4 Consensus size: 79
33108954 CCTAGTGTCT
* * * * *
33108964 TTCCTAATTAATATGGAACTCACATCATTTTTCGACTCCATTGTATGTAGAATATATCAATTCCA
1 TTCCTAATCAATATGGAACTCACATGATTTTCCGACTCCATTGTATATAGAACATATCAATTCCA
*
33109029 AAATCTCTTTGCCC
66 AAACCTCTTTGCCC
* * *
33109043 TTCCTAACCAATATGGAACTCACATGATTTTCCGACTCCATTATACATAGAACATATCAATTCCA
1 TTCCTAATCAATATGGAACTCACATGATTTTCCGACTCCATTGTATATAGAACATATCAATTCCA
*
33109108 AGACCTCTTTGCCC
66 AAACCTCTTTGCCC
* * * * *
33109122 TTCTTAACCAATATAGG-ACCCACGTTG-CTTTCCGACTCC-----AT-T-GAACATATCAA--C
1 TTCCTAATCAATAT-GGAACTCAC-ATGATTTTCCGACTCCATTGTATATAGAACATATCAATTC
* * *
33109176 TAAGACCTCTTT-ACC
64 CAAAACCTCTTTGCCC
* * ** * * *
33109191 TTCCAAATCAATATGGAACTTGTCACATCATTTTCTAACTCCACTGTACATAGAACATATCATTT
1 TTCCTAATCAATATGGAAC---TCACATGATTTTCCGACTCCATTGTATATAGAACATATCAATT
* * *
33109256 CCAATACCTCTTCGCAC
63 CCAAAACCTCTTTGCCC
* * * * *
33109273 TTCCTAACCAATATAG-ACCCTACATCGCTTTT-CGACTCC-----A-A-GGAACATATCAA--C
1 TTCCTAATCAATATGGAACTC-ACAT-GATTTTCCGACTCCATTGTATATAGAACATATCAATTC
** *
33109327 CAAGTCCTCCTTG-CC
64 CAAAACCTCTTTGCCC
* * * * * * *
33109342 TTCCTAATCAATACGGAACTCACATCG-TTTT-TGATTCAATTGTATGTAGAATATATAAATTCC
1 TTCCTAATCAATATGGAACTCACAT-GATTTTCCGACTCCATTGTATATAGAACATATCAATTCC
*
33109405 AAAACCTCTTTTCCC
65 AAAACCTCTTTGCCC
* *
33109420 TTCCTAATCAATATGGAAACTCACATCG-TTTTCCGACTCCATTGTACATAAAACATATCAATTC
1 TTCCTAATCAATATGG-AACTCACAT-GATTTTCCGACTCCATTGTATATAGAACATATCAATTC
* *
33109484 CAATACCTCTTCGCCC
64 CAAAACCTCTTTGCCC
* * * * * * * *
33109500 TTCCT-ACCAATATGGGACTCATATCG-TTTTCCAACT---TTAT-TAAAGAACATGTCGA--CC
1 TTCCTAATCAATATGGAACTCACAT-GATTTTCCGACTCCATTGTATATAGAACATATCAATTCC
*
33109557 AAGAA-CTCTTTTCCC
65 AA-AACCTCTTTGCCC
* * ** * * *
33109572 TTCCTAATGAATATGAAACTCACACCATTTTTCGACTCCATTGTATAAAGAACATATCAATTTCA
1 TTCCTAATCAATATGGAACTCACATGATTTTCCGACTCCATTGTATATAGAACATATCAATTCCA
* * ***
33109637 ATACCTCCTCATCC
66 AAACCTCTTTGCCC
* * * * * * * **
33109651 TTCCTAACCAATATGTG-ACTCACATCATTTTCCAACTCTACTATATTAAAGAACATATTGA--C
1 TTCCTAATCAATATG-GAACTCACATGATTTTCCGACTCCATTGTA-TATAGAACATATCAATTC
* * *
33109713 CAAGACCTCATTACCC
64 CAAAACCTCTTTGCCC
* * * *
33109729 -TCCGTAATCAATATGGAACTCACATTGTTTTTTCGACTCCATTGTATGTAGAAGATATCAATTC
1 TTCC-TAATCAATATGGAACTCACA-TGATTTTCCGACTCCATTGTATATAGAACATATCAATTC
*
33109793 CAATACCTCTTTGCCC
64 CAAAACCTCTTTGCCC
* * *
33109809 TTCCTAATCAATATGGGACTCGCATCATTTTC
1 TTCCTAATCAATATGGAACTCACATGATTTTC
33109841 TAACTCCACA
Statistics
Matches: 605, Mismatches: 143, Indels: 100
0.71 0.17 0.12
Matches are distributed among these distances:
68 10 0.02
69 35 0.06
70 25 0.04
71 1 0.00
72 50 0.08
73 25 0.04
74 12 0.02
75 12 0.02
76 3 0.00
77 28 0.05
78 77 0.13
79 204 0.34
80 94 0.16
81 15 0.02
82 14 0.02
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (79 bp):
TTCCTAATCAATATGGAACTCACATGATTTTCCGACTCCATTGTATATAGAACATATCAATTCCA
AAACCTCTTTGCCC
Found at i:33109224 original size:151 final size:148
Alignment explanation
Indices: 33109041--33109469 Score: 468
Period size: 151 Copynumber: 2.9 Consensus size: 148
33109031 ATCTCTTTGC
* * * *
33109041 CCTTCCTAACCAATATGGAACTCACATGATTTTCCGACTCCATTATACATAGAACATATCAATTC
1 CCTTCCTAATCAATATGGAACTCACATCATTTTCTGACTCCATTGTACATAGAACATATCAATTC
* * * *
33109106 CAAGACCTCTTTGCCCTTCTTAACCAATATAGGACCCACGTTGCTTTCCGACTCCATTGAACATA
66 CAAAACCTCTTTGCCCTTCCTAACCAATATAGGACCCACATCGCTTTCCGACTCCATTGAACATA
* *
33109171 TCAACTAAGACCTCTTTA
131 TCAACCAAGACCTCCTTA
* * * *
33109189 CCTTCCAAATCAATATGGAACTTGTCACATCATTTTCTAACTCCACTGTACATAGAACATATCAT
1 CCTTCCTAATCAATATGGAAC---TCACATCATTTTCTGACTCCATTGTACATAGAACATATCAA
* * * * **
33109254 TTCCAATACCTCTTCGCACTTCCTAACCAATATA-GACCCTACATCGCTTTTCGACTCCAAGGAA
63 TTCCAAAACCTCTTTGCCCTTCCTAACCAATATAGGACCC-ACATCGCTTTCCGACTCCATTGAA
* *
33109318 CATATCAACCAAGTCCTCCTTG
127 CATATCAACCAAGACCTCCTTA
* * * * ** * *
33109340 CCTTCCTAATCAATACGGAACTCACATCGTTTT-TGATTCAATTGTATGTAGAATATATAAATTC
1 CCTTCCTAATCAATATGGAACTCACATCATTTTCTGACTCCATTGTACATAGAACATATCAATTC
* * * * *
33109404 CAAAACCTCTTTTCCCTTCCTAATCAATAT-GGAAACTCACATCGTTTTCCGACTCCATTGTACA
66 CAAAACCTCTTTGCCCTTCCTAACCAATATAGG--ACCCACATCGCTTTCCGACTCCATTGAACA
33109468 TA
129 TA
33109470 AAACATATCA
Statistics
Matches: 230, Mismatches: 44, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
147 48 0.21
148 53 0.23
149 3 0.01
150 5 0.02
151 121 0.53
ACGTcount: A:0.31, C:0.29, G:0.09, T:0.32
Consensus pattern (148 bp):
CCTTCCTAATCAATATGGAACTCACATCATTTTCTGACTCCATTGTACATAGAACATATCAATTC
CAAAACCTCTTTGCCCTTCCTAACCAATATAGGACCCACATCGCTTTCCGACTCCATTGAACATA
TCAACCAAGACCTCCTTA
Found at i:33109492 original size:80 final size:79
Alignment explanation
Indices: 33109340--33109840 Score: 368
Period size: 80 Copynumber: 6.4 Consensus size: 79
33109330 GTCCTCCTTG
* * * * * * * *
33109340 CCTTCCTAATCAATACGGAACTCACATCGTTTT-TGATTCAATTGTATGTAGAATATATAAATTC
1 CCTTCCTAATCAATATGGAACTCACATCGTTTTCCGACTCCATTGTATATAAAACATATCAATTC
*
33109404 CAAAACCTCTTTTC
66 CAATACCTCTTTTC
*
33109418 CCTTCCTAATCAATATGGAAACTCACATCGTTTTCCGACTCCATTGTACATAAAACATATCAATT
1 CCTTCCTAATCAATATGG-AACTCACATCGTTTTCCGACTCCATTGTATATAAAACATATCAATT
**
33109483 CCAATACCTCTTCGC
65 CCAATACCTCTTTTC
* * * * * * *
33109498 CCTTCCT-ACCAATATGGGACTCATATCGTTTTCCAACT---TTAT-TA-AAGAACATGTCGA--
1 CCTTCCTAATCAATATGGAACTCACATCGTTTTCCGACTCCATTGTATATAA-AACATATCAATT
* *
33109555 CCAAGAACTCTTTTC
65 CCAATACCTCTTTTC
* * * * *
33109570 CCTTCCTAATGAATATGAAACTCACACCATTTTTCGACTCCATTGTATA-AAGAACATATCAATT
1 CCTTCCTAATCAATATGGAACTCACATCGTTTTCCGACTCCATTGTATATAA-AACATATCAATT
* **
33109634 TCAATACCTCCTCAT-
65 CCAATACCT-CTTTTC
* * * * * * **
33109649 CCTTCCTAACCAATATGTG-ACTCACATCATTTTCCAACTCTACTATAT-TAAAGAACATATTGA
1 CCTTCCTAATCAATATG-GAACTCACATCGTTTTCCGACTCCATTGTATAT-AA-AACATATCAA
* * *
33109712 --CCAAGACCTCATTAC
63 TTCCAATACCTCTTTTC
* * * * *
33109727 CC-TCCGTAATCAATATGGAACTCACATTGTTTTTTCGACTCCATTGTATGTAGAAGATATCAAT
1 CCTTCC-TAATCAATATGGAACTCACATCG-TTTTCCGACTCCATTGTATATAAAACATATCAAT
*
33109791 TCCAATACCTCTTTGC
64 TCCAATACCTCTTTTC
* * *
33109807 CCTTCCTAATCAATATGGGACTCGCATCATTTTC
1 CCTTCCTAATCAATATGGAACTCACATCGTTTTC
33109841 TAACTCCACA
Statistics
Matches: 323, Mismatches: 78, Indels: 43
0.73 0.18 0.10
Matches are distributed among these distances:
72 18 0.06
73 24 0.07
74 9 0.03
75 3 0.01
76 3 0.01
77 18 0.06
78 69 0.21
79 87 0.27
80 89 0.28
81 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (79 bp):
CCTTCCTAATCAATATGGAACTCACATCGTTTTCCGACTCCATTGTATATAAAACATATCAATTC
CAATACCTCTTTTC
Found at i:33109659 original size:378 final size:378
Alignment explanation
Indices: 33108964--33109840 Score: 993
Period size: 378 Copynumber: 2.3 Consensus size: 378
33108954 CCTAGTGTCT
* *
33108964 TTCCTAATTAATATGGAACTCACATCATTTTTCGACTCCATTGTATGTAGAATATATCAATTCCA
1 TTCCTAATCAATATGGAACTCACATCGTTTTTCGACTCCATTGTATGTAGAATATATCAATTCCA
* * *
33109029 AAATCTCTTTGCCCTTCCTAACCAATATGGAACTCACATGATTTTCCGACTCCATTATACATAGA
66 AAACCTCTTTGCCCTTCCTAATCAATATGGAACTCACATGATTTTCCGACTCCATTATACATAAA
* * * * *
33109094 ACATATCAATTCCAAGACCTCTTTGCCCTTCTTAACCAATATAGGACCCACGTTGCTTTCCGACT
131 ACATATCAATTCCAAGACCTCTTCGCCCTTCCTAACCAATATAGGACCCACATCGCTTTCCAACT
* * * *
33109159 CCATTGAACATATCAACTAAGACCTCTTTACCTTCCAAATCAATATGGAACTTGTCACATCATTT
196 CCATTGAACATATCAACCAAGAACTCTTTACCTTCCAAATCAATATGAAAC-T-TCACACCATTT
* *
33109224 TCTAACTCCACTGTACATAGAACATATCATTTCCAATACCTCTTCGCACTTCCTAACCAATAT-A
259 TCTAACTCCACTGTACAAAGAACATATCATTTCCAATACCTCCTCGCACTTCCTAACCAATATGA
* * * * * *
33109288 GACCCTACATCGCTTTT-CGACTC-C-AAGGAACATATCAACCAAGTCCTCCTTGCC
324 GACCC-ACATC-ATTTTCCAACTCACTAAAGAACATATCAACCAAGACCTCATTACC
* * * *
33109342 TTCCTAATCAATACGGAACTCACATCGTTTTT-GATTCAATTGTATGTAGAATATATAAATTCCA
1 TTCCTAATCAATATGGAACTCACATCGTTTTTCGACTCCATTGTATGTAGAATATATCAATTCCA
* *
33109406 AAACCTCTTTTCCCTTCCTAATCAATATGGAAACTCACATCG-TTTTCCGACTCCATTGTACATA
66 AAACCTCTTTGCCCTTCCTAATCAATATGG-AACTCACAT-GATTTTCCGACTCCATTATACATA
* * * * *
33109470 AAACATATCAATTCCAATACCTCTTCGCCCTTCCT-ACCAATATGGGACTCATATCGTTTTCCAA
129 AAACATATCAATTCCAAGACCTCTTCGCCCTTCCTAACCAATATAGGACCCACATCGCTTTCCAA
** * * * * *
33109534 CTTTATTAAAGAACATGTCGACCAAGAACTCTTTTCCCTTCCTAATGAATATGAAAC-TCACACC
194 CTCCATT---GAACATATCAACCAAGAACTC-TTTACCTTCCAAATCAATATGAAACTTCACACC
* * * *
33109598 ATTTT-TCGACTCCATTGTATAAAGAACATATCAATTT-CAATACCTCCTCATC-CTTCCTAACC
255 ATTTTCT-AACTCCACTGTACAAAGAACATATC-ATTTCCAATACCTCCTC-GCACTTCCTAACC
* * **
33109660 AATATGTGACTCACATCATTTTCCAACTCTACTATATTAAAGAACATATTGACCAAGACCTCATT
317 AATATGAGACCCACATCATTTTCCAACTC-AC-----TAAAGAACATATCAACCAAGACCTCATT
33109725 ACC
376 ACC
* * *
33109728 CTCCGTAATCAATATGGAACTCACATTGTTTTTTCGACTCCATTGTATGTAGAAGATATCAATTC
1 TTCC-TAATCAATATGGAACTCACATCG-TTTTTCGACTCCATTGTATGTAGAATATATCAATTC
* * * *
33109793 CAATACCTCTTTGCCCTTCCTAATCAATATGGGACTCGCATCATTTTC
64 CAAAACCTCTTTGCCCTTCCTAATCAATATGGAACTCACATGATTTTC
33109841 TAACTCCACA
Statistics
Matches: 416, Mismatches: 60, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
377 88 0.21
378 158 0.38
379 10 0.02
380 18 0.04
381 21 0.05
386 27 0.06
387 21 0.05
388 17 0.04
389 56 0.13
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (378 bp):
TTCCTAATCAATATGGAACTCACATCGTTTTTCGACTCCATTGTATGTAGAATATATCAATTCCA
AAACCTCTTTGCCCTTCCTAATCAATATGGAACTCACATGATTTTCCGACTCCATTATACATAAA
ACATATCAATTCCAAGACCTCTTCGCCCTTCCTAACCAATATAGGACCCACATCGCTTTCCAACT
CCATTGAACATATCAACCAAGAACTCTTTACCTTCCAAATCAATATGAAACTTCACACCATTTTC
TAACTCCACTGTACAAAGAACATATCATTTCCAATACCTCCTCGCACTTCCTAACCAATATGAGA
CCCACATCATTTTCCAACTCACTAAAGAACATATCAACCAAGACCTCATTACC
Found at i:33110530 original size:79 final size:77
Alignment explanation
Indices: 33110403--33110568 Score: 181
Period size: 79 Copynumber: 2.1 Consensus size: 77
33110393 ACATCACTTG
* * * * * * * *
33110403 TCGACTCCACTGTATTAAAGAACATATGAACCAATACCTCTTTGCCCTTCTTAATCAATATAGAA
1 TCGACTCCATTGTA-GATAGAACATATCAACCAAGACCTCTTTACCCTTCCTAAGCAATATAGAA
*
33110468 CTCATATAGTT-T
65 CTCACATAGTTGT
*
33110480 TACGACTCCATTGTAGATAGAACATATCAATTCCAAGACCTCTTTACCCTTCCTAAGCAATATGG
1 T-CGACTCCATTGTAGATAGAACATATCAA--CCAAGACCTCTTTACCCTTCCTAAGCAATATAG
* *
33110545 GACTCACATTGTTGT
63 AACTCACATAGTTGT
33110560 TCGACTCCA
1 TCGACTCCA
33110569 CTATAGAAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
77 13 0.18
78 12 0.16
79 46 0.63
80 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.32
Consensus pattern (77 bp):
TCGACTCCATTGTAGATAGAACATATCAACCAAGACCTCTTTACCCTTCCTAAGCAATATAGAAC
TCACATAGTTGT
Found at i:33111770 original size:18 final size:20
Alignment explanation
Indices: 33111732--33111772 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
33111722 TAACTTAAAT
*
33111732 TATTAATTAAGTAATTTCAA
1 TATTAAATAAGTAATTTCAA
33111752 TATTAAATAAGT-A-TTCAA
1 TATTAAATAAGTAATTTCAA
33111770 TAT
1 TAT
33111773 AATAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
TATTAAATAAGTAATTTCAA
Found at i:33116627 original size:2 final size:2
Alignment explanation
Indices: 33116616--33116707 Score: 168
Period size: 2 Copynumber: 46.5 Consensus size: 2
33116606 TCATGATAAT
33116616 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
33116657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33116699 TA TA TA TA T
1 TA TA TA TA T
33116708 TAAACATTAA
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
1 1 0.01
2 86 0.99
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33119878 original size:20 final size:20
Alignment explanation
Indices: 33119839--33119878 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33119829 CTAAACCTCC
*
33119839 AAACATTTACTTTTCCCCCA
1 AAACATTTACTTCTCCCCCA
* *
33119859 AAACTTTTACTTCTCTCCCA
1 AAACATTTACTTCTCCCCCA
33119879 TCCCACTCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.35, G:0.00, T:0.38
Consensus pattern (20 bp):
AAACATTTACTTCTCCCCCA
Found at i:33120182 original size:124 final size:125
Alignment explanation
Indices: 33120048--33120302 Score: 476
Period size: 124 Copynumber: 2.0 Consensus size: 125
33120038 ATTTTTCTCT
*
33120048 CCCCAATTTTTTTTTAATATTTTTCATCCAAAATTTTACTCTCCCTATTTATTTTCCCTCCGAAT
1 CCCCAATTTTTTTTTAATATTTTTCATCCAAAATTTTACTCTCCCTATTTATTTTCCCTCCAAAT
*
33120113 TTTACTCCCAAAACCCCCAAA-TTTTTATTTTCCCCTAAACTTTTACTTCTCACCCTTCA
66 TTTACTCCCAAAACCCCCAAATTTTTTATTTTCCCATAAACTTTTACTTCTCACCCTTCA
33120172 CCCCAATTTTTTTTTAATATTTTTCATCCAAAATTTTACTCTCCCTATTTATTTTCCCTCCAAAT
1 CCCCAATTTTTTTTTAATATTTTTCATCCAAAATTTTACTCTCCCTATTTATTTTCCCTCCAAAT
*
33120237 TTTACTCCCAAAACTCCCAAATTTTTTATTTTCCCATAAACTTTTACTTCTCACCCTTCA
66 TTTACTCCCAAAACCCCCAAATTTTTTATTTTCCCATAAACTTTTACTTCTCACCCTTCA
33120297 CCCCAA
1 CCCCAA
33120303 ATAAAAAATA
Statistics
Matches: 127, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
124 84 0.66
125 43 0.34
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (125 bp):
CCCCAATTTTTTTTTAATATTTTTCATCCAAAATTTTACTCTCCCTATTTATTTTCCCTCCAAAT
TTTACTCCCAAAACCCCCAAATTTTTTATTTTCCCATAAACTTTTACTTCTCACCCTTCA
Found at i:33120713 original size:19 final size:19
Alignment explanation
Indices: 33120689--33120726 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33120679 AAAGTTAATA
*
33120689 ACAAATTTGATTACAGTGG
1 ACAAATTTAATTACAGTGG
*
33120708 ACAAATTTAATTACGGTGG
1 ACAAATTTAATTACAGTGG
33120727 GTGATGGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
ACAAATTTAATTACAGTGG
Found at i:33124671 original size:2 final size:2
Alignment explanation
Indices: 33124664--33124698 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
33124654 TTTTGTATTG
33124664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
33124699 GGTGTTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33125973 original size:18 final size:16
Alignment explanation
Indices: 33125929--33125975 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
33125919 ATCCCTGAAT
33125929 TTTTTTTA-ATTTATA
1 TTTTTTTATATTTATA
*
33125944 TTTTTTAAATATTATATAA
1 TTTTTT-TATATT-TAT-A
33125963 TTTTTTTATATTT
1 TTTTTTTATATTT
33125976 TTTAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 6 0.23
16 1 0.04
17 4 0.15
18 8 0.31
19 7 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTTTATATTTATA
Found at i:33125976 original size:29 final size:29
Alignment explanation
Indices: 33125938--33125998 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
33125928 TTTTTTTTAA
33125938 TTTATATTTTTTAAATATTATATAATTTT
1 TTTATATTTTTTAAATATTATATAATTTT
33125967 TTTATATTTTTTAAATATTATATAATTTT
1 TTTATATTTTTTAAATATTATATAATTTT
33125996 TTT
1 TTT
33125999 TAAAAAATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTATATTTTTTAAATATTATATAATTTT
Found at i:33125995 original size:18 final size:18
Alignment explanation
Indices: 33125940--33125996 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
33125930 TTTTTTAATT
*
33125940 TATATTTTTTAAATATTA
1 TATAATTTTTAAATATTA
33125958 TATAA-TTTT---T-TTA
1 TATAATTTTTAAATATTA
33125971 TAT--TTTTTAAATATTA
1 TATAATTTTTAAATATTA
33125987 TATAATTTTT
1 TATAATTTTT
33125997 TTTAAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 1 0.03
15 1 0.03
16 6 0.19
17 4 0.13
18 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TATAATTTTTAAATATTA
Found at i:33137280 original size:18 final size:18
Alignment explanation
Indices: 33137232--33137274 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
33137222 TAATCTATTT
*
33137232 TTAATCAAATTAAATCGA
1 TTAATCAAATTAAATCAA
33137250 TTAATCAAATTAAATCAA
1 TTAATCAAATTAAATCAA
33137268 TTCAATC
1 TT-AATC
33137275 GATTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (18 bp):
TTAATCAAATTAAATCAA
Found at i:33137675 original size:8 final size:8
Alignment explanation
Indices: 33137664--33137690 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
33137654 TTTCATGAAA
33137664 TTTTTATT
1 TTTTTATT
33137672 TTTTTATT
1 TTTTTATT
33137680 TTTTTATT
1 TTTTTATT
33137688 TTT
1 TTT
33137691 CATCACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:33138348 original size:29 final size:32
Alignment explanation
Indices: 33138296--33138358 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 32
33138286 TAGTAAAAAT
* *
33138296 AAAATTATATTTTAATCTCTTTTAAAATTGTA
1 AAAATTATAATTTAATCTCTTTTAAAATTATA
33138328 AAAATT-TAATTTAATC-C-TTTAAAATTATA
1 AAAATTATAATTTAATCTCTTTTAAAATTATA
33138357 AA
1 AA
33138359 TATATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 13 0.45
30 1 0.03
31 9 0.31
32 6 0.21
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (32 bp):
AAAATTATAATTTAATCTCTTTTAAAATTATA
Found at i:33143760 original size:28 final size:28
Alignment explanation
Indices: 33143728--33143789 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
33143718 TAAGTCGTAA
* *
33143728 ATTTTATCATTTTGAAAATTTTAAATAT
1 ATTTTAGCATTTTCAAAATTTTAAATAT
* *
33143756 ATTTTAGCATTTTCATATTTTTAAATAT
1 ATTTTAGCATTTTCAAAATTTTAAATAT
33143784 -TTTTAG
1 ATTTTAG
33143790 TAATTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (28 bp):
ATTTTAGCATTTTCAAAATTTTAAATAT
Found at i:33143802 original size:27 final size:28
Alignment explanation
Indices: 33143736--33143813 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 28
33143726 AAATTTTATC
* * *
33143736 ATTTTGAAAATTTTAAATATATTTTAGC
1 ATTTTCAAATTTTTAAATATATTTTAGA
*
33143764 ATTTTCATATTTTTAAATAT-TTTTAGTA
1 ATTTTCAAATTTTTAAATATATTTTAG-A
*
33143792 ATTTT-AAATTTTTTGAATATAT
1 ATTTTCAAA-TTTTTAAATATAT
33143814 ATATATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
27 8 0.20
28 32 0.78
29 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (28 bp):
ATTTTCAAATTTTTAAATATATTTTAGA
Found at i:33143959 original size:18 final size:18
Alignment explanation
Indices: 33143936--33143970 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33143926 TATCAATTTG
*
33143936 TTATTCGAGTTATTCAAA
1 TTATTCGAATTATTCAAA
33143954 TTATTCGAATTATTCAA
1 TTATTCGAATTATTCAA
33143971 GTTGTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (18 bp):
TTATTCGAATTATTCAAA
Found at i:33154275 original size:31 final size:31
Alignment explanation
Indices: 33154176--33154267 Score: 121
Period size: 31 Copynumber: 3.0 Consensus size: 31
33154166 ACAAAAAAAA
* * *
33154176 AGTTTAAATTCCAATATGAAAATAATTGTTT
1 AGTTTAAACTCCAATATAAAAATAATTGTCT
* *
33154207 AGTTTAAGCTCCAATATAAAAATAATTATCT
1 AGTTTAAACTCCAATATAAAAATAATTGTCT
* *
33154238 AGTTTAAACTCTAATGTAAAAATAATTGTC
1 AGTTTAAACTCCAATATAAAAATAATTGTC
33154268 AAATTTAAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (31 bp):
AGTTTAAACTCCAATATAAAAATAATTGTCT
Found at i:33164596 original size:9 final size:9
Alignment explanation
Indices: 33164582--33164680 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 9
33164572 ACAAATGATT
33164582 TTAAAATTA
1 TTAAAATTA
33164591 TTAAAATTA
1 TTAAAATTA
33164600 TTTTTAAAA--A
1 ---TTAAAATTA
* *
33164610 ATAAAATTG
1 TTAAAATTA
33164619 TTAAAATTA
1 TTAAAATTA
33164628 TTTTAAAATTAA
1 --TTAAAATT-A
33164640 TTTAAAATTA
1 -TTAAAATTA
33164650 TTTTGTAAAA-TA
1 ---T-TAAAATTA
33164662 -TAAAATTA
1 TTAAAATTA
33164670 TTAAAATTA
1 TTAAAATTA
33164679 TT
1 TT
33164681 TTAATATTTT
Statistics
Matches: 73, Mismatches: 4, Indels: 26
0.71 0.04 0.25
Matches are distributed among these distances:
7 10 0.14
8 2 0.03
9 26 0.36
10 2 0.03
11 17 0.23
12 11 0.15
13 5 0.07
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:33164635 original size:11 final size:11
Alignment explanation
Indices: 33164574--33164684 Score: 67
Period size: 11 Copynumber: 10.1 Consensus size: 11
33164564 TCACATCAAC
*
33164574 AAATGATTTTA
1 AAATTATTTTA
33164585 AAATTA--TTA
1 AAATTATTTTA
33164594 AAATTATTTTTAAA
1 AAATTA-TTTT--A
*
33164608 AAATAAAATTGTTA
1 AAAT--TATT-TTA
33164622 AAATTATTTTA
1 AAATTATTTTA
*
33164633 AAATTAATTTA
1 AAATTATTTTA
33164644 AAATTATTTTGTA
1 AAATTA-TTT-TA
33164657 AAA-TA---TA
1 AAATTATTTTA
33164664 AAATTA--TTA
1 AAATTATTTTA
33164673 AAATTATTTTA
1 AAATTATTTTA
33164684 A
1 A
33164685 TATTTTAATC
Statistics
Matches: 81, Mismatches: 5, Indels: 28
0.71 0.04 0.25
Matches are distributed among these distances:
7 5 0.06
8 2 0.02
9 17 0.21
11 28 0.35
12 9 0.11
13 5 0.06
14 10 0.12
15 2 0.02
16 3 0.04
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:33164668 original size:51 final size:48
Alignment explanation
Indices: 33164574--33164692 Score: 168
Period size: 51 Copynumber: 2.4 Consensus size: 48
33164564 TCACATCAAC
* *
33164574 AAATGATTTTAAAATTATTAAAATTATTTTTAAAAAATAAAATTGTTA
1 AAATTATTTTAAAATTATTAAAATTATTTTTAAAAAATAAAATTATTA
*
33164622 AAATTATTTTAAAATTAATTTAAAATTATTTTGTAAAATATAAAATTATTA
1 AAATTATTTTAAAATT-A-TTAAAATTATTTT-TAAAAAATAAAATTATTA
*
33164673 AAATTATTTTAATATT-TTAA
1 AAATTATTTTAAAATTATTAA
33164693 TCATCATCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
48 19 0.30
49 1 0.02
50 13 0.20
51 31 0.48
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (48 bp):
AAATTATTTTAAAATTATTAAAATTATTTTTAAAAAATAAAATTATTA
Found at i:33166025 original size:27 final size:26
Alignment explanation
Indices: 33165995--33166049 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
33165985 AAAACTCATC
33165995 GGAA-GGAAAATAAGAAGAAGGGGAAGG
1 GGAAGGGAAAA-AAGAAG-AGGGGAAGG
* *
33166022 GGAAGGGGAAAGAGAAGAGGGGAAGG
1 GGAAGGGAAAAAAGAAGAGGGGAAGG
33166048 GG
1 GG
33166050 GGAAGAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 9 0.36
28 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.53, T:0.02
Consensus pattern (26 bp):
GGAAGGGAAAAAAGAAGAGGGGAAGG
Found at i:33166112 original size:11 final size:11
Alignment explanation
Indices: 33166082--33166160 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
33166072 ATAATTTTAT
33166082 ATTTTAAAAATA
1 ATTTT-AAAATA
* *
33166094 ATTCTAAATTA
1 ATTTTAAAATA
33166105 ATTTTAAAATA
1 ATTTTAAAATA
33166116 ATTTT--AATA
1 ATTTTAAAATA
33166125 ATTTT---ATA
1 ATTTTAAAATA
*
33166133 TTTTTAAAAAATA
1 ATTTT--AAAATA
*
33166146 ATTTTAAAATC
1 ATTTTAAAATA
33166157 ATTT
1 ATTT
33166161 GCTGACGTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
8 7 0.13
9 9 0.16
11 28 0.51
12 4 0.07
13 7 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:33166845 original size:6 final size:6
Alignment explanation
Indices: 33166827--33166935 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
33166817 TAAATTAGTT
* *
33166827 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
33166874 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA-A
*
33166923 TTAAAAA TTTAAA
1 TT-TAAA TTTAAA
33166936 GCCCAATGTC
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 15 0.18
8 6 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:33166859 original size:17 final size:15
Alignment explanation
Indices: 33166831--33166895 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 15
33166821 TTAGTTTTTA
33166831 AATTTATTTAAATTT
1 AATTTATTTAAATTT
33166846 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
*
33166863 AA-ATATTTAAATTT
1 AATTTATTTAAATTT
33166877 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
33166894 AA
1 AA
33166896 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.26
15 4 0.09
16 6 0.14
17 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:33166873 original size:31 final size:31
Alignment explanation
Indices: 33166835--33166898 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
33166825 TTTTTAAATT
*
33166835 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
33166866 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
33166897 TA
1 TA
33166899 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:33166876 original size:25 final size:25
Alignment explanation
Indices: 33166842--33166891 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
33166832 ATTTATTTAA
* *
33166842 ATTTAGATTTATTTTAAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAT
*
33166867 ATTTAAATTTAATTTGAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAT
33166892 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTTAAATTTAATTTAAATTTAAAT
Found at i:33166889 original size:11 final size:11
Alignment explanation
Indices: 33166827--33166897 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
33166817 TAAATTAGTT
33166827 TTTAAATTT-A
1 TTTAAATTTAA
33166837 TTTAAATTTAGA
1 TTTAAATTTA-A
*
33166849 TTT-ATTTTAAA
1 TTTAAATTT-AA
33166860 TTTAAA--T-A
1 TTTAAATTTAA
33166868 TTTAAATTTAA
1 TTTAAATTTAA
*
33166879 TTTGAATTTAAA
1 TTTAAATTT-AA
33166891 TTTAAAT
1 TTTAAAT
33166898 AAAAATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
8 7 0.14
10 11 0.22
11 17 0.35
12 14 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:33166894 original size:42 final size:41
Alignment explanation
Indices: 33166827--33166927 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
33166817 TAAATTAGTT
* ** * *
33166827 TTTAAATTT-ATTTAAATTTAGATTTATTTTAAATTTAAATA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
33166868 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
33166909 TATTAAATTTAATATTAAA
1 T-TTAAATTTAAT-TTAAA
33166928 AATTTAAAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 11 0.22
42 35 0.70
43 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (41 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:33167127 original size:15 final size:15
Alignment explanation
Indices: 33167107--33167137 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
33167097 GCCTATGCTG
33167107 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
33167122 CTGCCACCACCAGCT
1 CTGCCACCACCAGCT
33167137 C
1 C
33167138 CATCCACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.55, G:0.13, T:0.13
Consensus pattern (15 bp):
CTGCCACCACCAGCT
Found at i:33167593 original size:30 final size:30
Alignment explanation
Indices: 33167557--33167695 Score: 233
Period size: 30 Copynumber: 4.6 Consensus size: 30
33167547 AAATTGTCTA
* * *
33167557 AAAATTACATTTTGACCTCAAAACTTTCCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
33167587 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
* *
33167617 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
33167647 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTATATTTTGACCCCAAAACTTTTCC
33167677 AAAATTATATTTTGACCCC
1 AAAATTATATTTTGACCCC
33167696 CGGAGCTTCT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 102 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCAAAACTTTTCC
Found at i:33167873 original size:59 final size:59
Alignment explanation
Indices: 33167677--33167871 Score: 209
Period size: 59 Copynumber: 3.3 Consensus size: 59
33167667 AAACTTTTCC
* * * * **
33167677 AAAATTA-TATTTTGACCCCCGGAGCTTCTAAAATT--TTGTTTTAACCACAATTTTACCG
1 AAAATTACCATTTT-ACCCCCGAAGCTTCTAAAATTCCAT-TTTTAACCCCAATTACACCG
* * * *
33167735 AAAATTACCATTTTATCCCCGAAGCTTCTAAAATTTCATTTTTAACCCTAATTTCACCG
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACACCG
* * * *
33167794 AAAATTGCCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACACCG
*
33167852 AAAATTACCATGTTACCCCC
1 AAAATTACCATTTTACCCCC
33167872 CGGGTATCCA
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
58 44 0.38
59 72 0.62
60 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCAATTACACCG
Found at i:33179855 original size:68 final size:68
Alignment explanation
Indices: 33179746--33180517 Score: 1357
Period size: 68 Copynumber: 11.3 Consensus size: 68
33179736 GGTCACCAAT
* * * *
33179746 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33179811 AAC
66 AAC
33179814 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33179879 AAC
66 AAC
33179882 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33179947 AAC
66 AAC
33179950 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180015 AAC
66 AAC
*
33180018 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAAG
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG-AG
33180083 CAAC
65 CAAC
* * * *
33180087 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180152 AAC
66 AAC
33180155 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180220 AAC
66 AAC
33180223 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180288 AAC
66 AAC
*
33180291 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAAC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180356 AAC
66 AAC
*
33180359 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAAG
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG-AG
33180424 CAAC
65 CAAC
* * * * *
33180428 GTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAAGAGC
1 GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180493 AAC
66 AAC
*
33180496 GTCA-TCCTCTTGGAATTGAAGT
1 GTCATTCC-CTTGAAATTGAAGT
33180518 GAAGTTGGAT
Statistics
Matches: 679, Mismatches: 22, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
67 2 0.00
68 549 0.81
69 128 0.19
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (68 bp):
GTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAGAGC
AAC
Found at i:33180369 original size:341 final size:341
Alignment explanation
Indices: 33179746--33180517 Score: 1465
Period size: 341 Copynumber: 2.3 Consensus size: 341
33179736 GGTCACCAAT
33179746 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33179811 AACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
66 AACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
33179876 AGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
131 AGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
33179941 AAGAGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
196 AAGAGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
*
33180006 AGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAT
261 AGTAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAT
33180071 TGAAGTAAGAAGCAAC
326 TGAAGTAAGAAGCAAC
33180087 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
1 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
33180152 AACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
66 AACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
33180217 AGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
131 AGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
33180282 AAGAGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
196 AAGAGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
33180347 AGTAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAT
261 AGTAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAT
33180412 TGAAGTAAGAAGCAAC
326 TGAAGTAAGAAGCAAC
* * * * *
33180428 GTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTACCTCTGAAATTGAAGTAAGAGC
1 GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
*
33180493 AACGTCA-TCCTCTTGGAATTGAAGT
66 AACGTCATTCC-CTTGAAATTGAAGT
33180518 GAAGTTGGAT
Statistics
Matches: 423, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
340 3 0.01
341 420 0.99
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (341 bp):
GTCATCCCCTCGAAATTGATGTAGAGTGGATAGCACGTCTTCATCTCTGAAATTGAAGTAAGAGC
AACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGTAAG
AGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAGT
AAGAGCAACGTCATTCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGA
AGTAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAAT
TGAAGTAAGAAGCAAC
Found at i:33180825 original size:6 final size:6
Alignment explanation
Indices: 33180807--33180915 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
33180797 TAAATTGGTT
* *
33180807 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
33180854 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA-A
*
33180903 TTAAAAA TTTAAA
1 TT-TAAA TTTAAA
33180916 GCCCAATGTC
Statistics
Matches: 83, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 15 0.18
8 6 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:33180839 original size:17 final size:15
Alignment explanation
Indices: 33180811--33180875 Score: 78
Period size: 17 Copynumber: 4.1 Consensus size: 15
33180801 TTGGTTTTTA
33180811 AATTTATTTAAATTT
1 AATTTATTTAAATTT
33180826 AGATTTATTTTAAATTT
1 A-ATTTA-TTTAAATTT
*
33180843 AA-ATATTTAAATTT
1 AATTTATTTAAATTT
33180857 AATTTGAATTTAAATTT
1 AATTT--ATTTAAATTT
33180874 AA
1 AA
33180876 ATAAAAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.26
15 4 0.09
16 6 0.14
17 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTATTTAAATTT
Found at i:33180853 original size:31 final size:31
Alignment explanation
Indices: 33180815--33180878 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
33180805 TTTTTAAATT
*
33180815 TATTTAAATTTAGATTT-ATTTTAAATTTAAA
1 TATTTAAATTTA-ATTTGAATTTAAATTTAAA
33180846 TATTTAAATTTAATTTGAATTTAAATTTAAA
1 TATTTAAATTTAATTTGAATTTAAATTTAAA
33180877 TA
1 TA
33180879 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TATTTAAATTTAATTTGAATTTAAATTTAAA
Found at i:33180856 original size:25 final size:25
Alignment explanation
Indices: 33180822--33180871 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
33180812 ATTTATTTAA
* *
33180822 ATTTAGATTTATTTTAAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAT
*
33180847 ATTTAAATTTAATTTGAATTTAAAT
1 ATTTAAATTTAATTTAAATTTAAAT
33180872 TTAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTTAAATTTAATTTAAATTTAAAT
Found at i:33180869 original size:11 final size:11
Alignment explanation
Indices: 33180807--33180877 Score: 62
Period size: 11 Copynumber: 6.6 Consensus size: 11
33180797 TAAATTGGTT
33180807 TTTAAATTT-A
1 TTTAAATTTAA
33180817 TTTAAATTTAGA
1 TTTAAATTTA-A
*
33180829 TTT-ATTTTAAA
1 TTTAAATTT-AA
33180840 TTTAAA--T-A
1 TTTAAATTTAA
33180848 TTTAAATTTAA
1 TTTAAATTTAA
*
33180859 TTTGAATTTAAA
1 TTTAAATTT-AA
33180871 TTTAAAT
1 TTTAAAT
33180878 AAAAATTAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
8 7 0.14
10 11 0.22
11 17 0.35
12 14 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:33180874 original size:42 final size:41
Alignment explanation
Indices: 33180807--33180907 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
33180797 TAAATTGGTT
* ** * *
33180807 TTTAAATTT-ATTTAAATTTAGATTTATTTTAAATTTAAATA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAA-A
*
33180848 TTTAAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAA
1 TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
33180889 TATTAAATTTAATATTAAA
1 T-TTAAATTTAAT-TTAAA
33180908 AATTTAAAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 11 0.22
42 35 0.70
43 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (41 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAA
Found at i:33181558 original size:30 final size:30
Alignment explanation
Indices: 33181522--33181690 Score: 248
Period size: 30 Copynumber: 5.6 Consensus size: 30
33181512 AAATTGTCTA
* * *
33181522 AAAATTATATTTCAACCCTAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
33181552 AAAATTACATTTTAACCCTAAAACTTTCCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
33181582 AAAATTACATTTTGACCCAAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
33181612 AAAATTACATTTTAACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
*
33181642 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTAACCCCAAAACTTTTCC
* *
33181672 AAAATTATATTTTGACCCC
1 AAAATTACATTTTAACCCC
33181691 CGAAGCTTCT
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 129 1.00
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCAAAACTTTTCC
Found at i:33181675 original size:90 final size:90
Alignment explanation
Indices: 33181522--33181689 Score: 273
Period size: 90 Copynumber: 1.9 Consensus size: 90
33181512 AAATTGTCTA
* * *
33181522 AAAATTATATTTCAACCCTAAAACTTTTCCAAAATTACATTTTAACCCTAAAACTTTCCCAAAAT
1 AAAATTACATTTCAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTCCCAAAAT
33181587 TACATTTTGACCCAAAAACTTTTCC
66 TACATTTTGACCCAAAAACTTTTCC
* * *
33181612 AAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAAT
1 AAAATTACATTTCAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTCCCAAAAT
*
33181677 TATATTTTGACCC
66 TACATTTTGACCC
33181690 CCGAAGCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (90 bp):
AAAATTACATTTCAACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTTCCCAAAAT
TACATTTTGACCCAAAAACTTTTCC
Found at i:33181748 original size:58 final size:58
Alignment explanation
Indices: 33181672--33181866 Score: 225
Period size: 59 Copynumber: 3.3 Consensus size: 58
33181662 AAACTTTTCC
* * *
33181672 AAAATTA-TATTTTGACCCCCGAAGCTTCTAAAATTCC-GTTTTAACCTCGATTTTACCG
1 AAAATTACCATTTT-ACCCCCGAAGCTTCTAAAATTCCATTTTTAACC-CGATTTCACCG
* *
33181730 AAAATTACCATTTTACCCCCAAAGCTTCTAAAATTCCATTTTTAACCCTAATTTCACCG
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCC-GATTTCACCG
* * * * *
33181789 AAAATTGCCATTTTACCCTCGAATCTTTTAAAATTCCATTTTTAACCCCGATTACACC-
1 AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAA-CCCGATTTCACCG
* *
33181847 AAAATTACCATGTTGCCCCC
1 AAAATTACCATTTTACCCCC
33181867 CGGGTATCCA
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 46 0.39
59 68 0.58
60 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCGATTTCACCG
Found at i:33191106 original size:16 final size:17
Alignment explanation
Indices: 33191082--33191115 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33191072 CTGTTAACAG
33191082 TAACTAACAGTAACTAC
1 TAACTAACAGTAACTAC
*
33191099 TAAC-AACATTAACTAC
1 TAACTAACAGTAACTAC
33191115 T
1 T
33191116 TAGTCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (17 bp):
TAACTAACAGTAACTAC
Found at i:33194868 original size:24 final size:23
Alignment explanation
Indices: 33194837--33194913 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
33194827 ATATTATTCG
33194837 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCAATTA-ATGTTCA
* **
33194861 TGAACATGTTCATTTAATGTTTG
1 TGAACATGTTCAATTAATGTTCA
* *
33194884 TGAACATATTCAATTAA-GTTAAA
1 TGAACATGTTCAATTAATGTT-CA
33194907 TGAACAT
1 TGAACAT
33194914 ATTCGTGAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 3 0.07
23 27 0.60
24 15 0.33
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.40
Consensus pattern (23 bp):
TGAACATGTTCAATTAATGTTCA
Found at i:33194887 original size:23 final size:23
Alignment explanation
Indices: 33194833--33194900 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
33194823 ATTAATATTA
33194833 TTCGTGAACATGTTCAATTATATG
1 TTCGTGAACATGTTCAATTA-ATG
* *
33194857 TTCATGAACATGTTCATTTAATG
1 TTCGTGAACATGTTCAATTAATG
* *
33194880 TTTGTGAACATATTCAATTAA
1 TTCGTGAACATGTTCAATTAA
33194901 GTTAAATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (23 bp):
TTCGTGAACATGTTCAATTAATG
Found at i:33196549 original size:90 final size:90
Alignment explanation
Indices: 33196404--33196608 Score: 356
Period size: 90 Copynumber: 2.3 Consensus size: 90
33196394 AAATACAAAC
* *
33196404 ATAGAAATTGAACAGTTCTCTGAATCAAAGCCTCCTTTCTTTTAAAGAACAACCCTGACACCATC
1 ATAGAAATTGAACAGTTCTCTGAACCAAAGCCTCCTTTCTTTTAAAGAACAACCCTGACACCACC
*
33196469 AATTTCAATCTCCATCTATACATCT
66 AATTTCAATCTCCATCTATACATAT
33196494 ATAGAAATTGAACAGTTCTCTGAACCAAAGCCTCCTTTCTTTTAAAGAACAACCCTGACACCACC
1 ATAGAAATTGAACAGTTCTCTGAACCAAAGCCTCCTTTCTTTTAAAGAACAACCCTGACACCACC
33196559 AATTTCAATCTCCATCTATACATAT
66 AATTTCAATCTCCATCTATACATAT
* *
33196584 ATAGAAATTTCAACAGTTCTATGAA
1 ATAGAAA-TTGAACAGTTCTCTGAA
33196609 TCTAAACCCT
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
90 94 0.86
91 15 0.14
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.30
Consensus pattern (90 bp):
ATAGAAATTGAACAGTTCTCTGAACCAAAGCCTCCTTTCTTTTAAAGAACAACCCTGACACCACC
AATTTCAATCTCCATCTATACATAT
Found at i:33200072 original size:31 final size:30
Alignment explanation
Indices: 33200030--33200096 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
33200020 GTATATTTCG
* * * *
33200030 AATTTAATTTTTATATTTTTATT-TTTAGA
1 AATTTAGTTTTTTTATTTTTTTTATTTAAA
33200059 AATTTAGTTTTTTTATTTTTTTTAATTTAAA
1 AATTTAGTTTTTTTATTTTTTTT-ATTTAAA
33200090 AATTTAG
1 AATTTAG
33200097 GTCAATTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.62
31 12 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (30 bp):
AATTTAGTTTTTTTATTTTTTTTATTTAAA
Found at i:33202270 original size:6 final size:6
Alignment explanation
Indices: 33202259--33202319 Score: 122
Period size: 6 Copynumber: 10.2 Consensus size: 6
33202249 TCATGCATTT
33202259 GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA
1 GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA GGAGTA
33202307 GGAGTA GGAGTA G
1 GGAGTA GGAGTA G
33202320 CACCACCTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GGAGTA
Found at i:33207127 original size:25 final size:26
Alignment explanation
Indices: 33207085--33207136 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
33207075 ACGGTGGTAA
*
33207085 GAGATTACACTCTCAAAGAA-ACAAT
1 GAGATTACAATCTCAAAGAATACAAT
* *
33207110 GAGATTAGAATCTTAAAGAATACAAT
1 GAGATTACAATCTCAAAGAATACAAT
33207136 G
1 G
33207137 TTAGAAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (26 bp):
GAGATTACAATCTCAAAGAATACAAT
Found at i:33213428 original size:2 final size:2
Alignment explanation
Indices: 33213421--33213450 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
33213411 TTAACACGCG
33213421 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
33213451 TTGATAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:33228416 original size:21 final size:21
Alignment explanation
Indices: 33228375--33228416 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
33228365 GTAAAATAAA
* *
33228375 AAAAATTATTTCTAGTACAAT
1 AAAAATAATTTCTAATACAAT
33228396 AAAAATAATTT-TAATATCAAT
1 AAAAATAATTTCTAATA-CAAT
33228417 TATTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATAATTTCTAATACAAT
Found at i:33233497 original size:16 final size:15
Alignment explanation
Indices: 33233476--33233505 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
33233466 ACTTTAACAT
33233476 TAATATATCTATATAA
1 TAATATATC-ATATAA
33233492 TAATATATCATATA
1 TAATATATCATATA
33233506 TGTTAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATATCATATAA
Found at i:33239241 original size:18 final size:17
Alignment explanation
Indices: 33239220--33239253 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
33239210 ATTAATTTTT
33239220 TAAAATTATTAAAAATAA
1 TAAAATTA-TAAAAATAA
33239238 TAAAATTATAAAAATA
1 TAAAATTATAAAAATA
33239254 TCTTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Done.